id: E7F8B1 gene_symbol: si:dkey-283b1.7 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:7955 label: Danio rerio description: si:dkey-283b1.7 (ZFIN ZDB-GENE-120215-126, chromosome 3; RefSeq name Brorin) encodes a 242-residue predicted secreted protein of the brorin (VWC2/VWC2L) family. It has an N-terminal signal peptide, then a short linker and the family's conserved core of two chordin-like von Willebrand factor C (VWFC) cysteine-rich domains, followed by a short basic tail. All 20 core cysteines of human VWC2 are conserved, but the long N-terminal region that distinguishes VWC2 is absent, so the architecture resembles VWC2L. The core is about 55-60% identical to each of VWC2, VWC2L and zebrafish vwc2, which is much lower than the 84-89% identity between vwc2 and human or gar VWC2. PANTHER places it as a teleost-duplication co-ortholog of VWC2, paired with vwc2. Ensembl Compara instead gives it no gar or human ortholog, only a medaka one, and its chromosomal neighbourhood shows no conserved synteny with the gar vwc2 region. It is therefore a fast-evolving teleost member of the family whose exact origin is unresolved. Public RNA-Seq calls place its expression in retina and brain. No experimental study of the gene has been published. Its activity (BMP antagonism, as for Brorin) is inferred from family membership only. existing_annotations: - term: id: GO:0005576 label: extracellular region evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - MGI:MGI:2442987 - MGI:MGI:2444069 - PANTHER:PTN002921765 review: summary: Extracellular region (IBA, brorin family node). action: ACCEPT reason: The protein has a predicted signal peptide and no transmembrane segment, and family members are secreted. PANTHER node PTN002921765 covers both VWC2 and VWC2L (MGI donors Vwc2 and Vwc2l). si:dkey-283b1.7 falls inside the family whichever of the two branches it belongs to, so the inference does not depend on the unresolved orthology. supported_by: - &id001 reference_id: file:DANRE/si_dkey-283b1.7/si_dkey-283b1.7-bioinformatics/RESULTS.md supporting_text: si:dkey-283b1.7 has a predicted signal peptide (residues 1-18) - reference_id: PMID:17400546 supporting_text: 'Mouse Brorin protein produced in cultured cells was efficiently secreted into the culture medium.' - term: id: GO:0005576 label: extracellular region evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0243 review: summary: Extracellular region from the UniProt 'Secreted' keyword (ARBA). action: ACCEPT reason: Consistent with the predicted signal peptide. supported_by: - *id001 - term: id: GO:0030514 label: negative regulation of BMP signaling pathway evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:2442987 - MGI:MGI:2444069 - PANTHER:PTN002921765 review: summary: Negative regulation of BMP signaling pathway (IBA, brorin family node). action: ACCEPT reason: BMP antagonism is shown for mouse Brorin and Brorin-like and for zebrafish vwc2. si:dkey-283b1.7 keeps the cysteine-rich core that carries the chordin-like domains, and nothing argues for loss of the function. It has not been tested for this gene. Its core is divergent (about 55-60% identity to other members), so the activity may differ quantitatively. PANTHER node PTN002921765 covers both VWC2 and VWC2L (MGI donors Vwc2 and Vwc2l). si:dkey-283b1.7 falls inside the family whichever of the two branches it belongs to, so the inference does not depend on the unresolved orthology. supported_by: - &id003 reference_id: file:DANRE/si_dkey-283b1.7/si_dkey-283b1.7-bioinformatics/RESULTS.md supporting_text: si:dkey-283b1.7 keeps all 20 core cysteines of human VWC2 - reference_id: PMID:17400546 supporting_text: 'The protein inhibited the activity of bone morphogenetic protein 2 (BMP2) and BMP6 in mouse preosteoblastic MC3T3-E1 cells.' - reference_id: PMID:28448525 supporting_text: These results indicate that the overexpression of brorin leads to the inactivation of Bmp signaling. - term: id: GO:0032281 label: AMPA glutamate receptor complex evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: part_of supporting_entities: - MGI:MGI:2442987 - MGI:MGI:2444069 - PANTHER:PTN002921765 review: summary: AMPA glutamate receptor complex (IBA from mouse Vwc2/Vwc2l proteomics). action: KEEP_AS_NON_CORE reason: Mouse Brorin and Brorin-like are peripheral extracellular constituents of native AMPA receptor complexes. The family inference is reasonable and the gene is expressed in brain and retina, but there is no zebrafish test, and the divergent sequence gives no assurance that the AMPAR/Noelin interaction is kept. Non-core. supported_by: - &id002 reference_id: PMID:37591201 supporting_text: Brorin and Brorin-like have been consistently retrieved in previous anti-GluA APs - reference_id: PMID:37591201 supporting_text: were entirely deprived of both Nrn1 and Brorin (Figure 1D) - &id004 reference_id: file:DANRE/si_dkey-283b1.7/si_dkey-283b1.7-bioinformatics/RESULTS.md supporting_text: si:dkey-283b1.7 has Bgee RNA-Seq calls in retina, brain and whole larva - term: id: GO:0045202 label: synapse evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0258 review: summary: Synapse from the UniProt ARBA subcellular location rule. action: KEEP_AS_NON_CORE reason: Follows from the AMPA receptor association of mammalian family members. Untested for this gene. supported_by: - *id002 references: - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000044 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt findings: [] - id: PMID:17400546 title: Brorin, a novel secreted bone morphogenetic protein antagonist, promotes neurogenesis in mouse neural precursor cells. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Mouse Brorin; family-level background only. - id: PMID:28448525 title: Brorin is required for neurogenesis, gliogenesis, and commissural axon guidance in the zebrafish forebrain. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Studies the paralog vwc2 only; si:dkey-283b1.7 is not mentioned. - id: PMID:37591201 title: A Noelin-organized extracellular network of proteins required for constitutive and context-dependent anchoring of AMPA-receptors. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Mouse; family-level background for the AMPAR rows. - id: file:DANRE/si_dkey-283b1.7/si_dkey-283b1.7-bioinformatics/RESULTS.md title: si:dkey-283b1.7 / vwc2 protein, synteny, expression and morpholino analyses reference_review: relevance: HIGH correctness: VERIFIED review_notes: Manual audit verified this sidecar supports si:dkey-283b1.7 as a secreted brorin-family protein with an intact cysteine-rich core while documenting that synteny does not establish it as a vwc2 TGD ohnolog. findings: - statement: Core cysteines conserved; VWC2-specific N-terminal region absent. supporting_text: si:dkey-283b1.7 keeps all 20 core cysteines of human VWC2 - statement: Expressed in retina and brain (Bgee RNA-Seq). supporting_text: si:dkey-283b1.7 has Bgee RNA-Seq calls in retina, brain and whole larva core_functions: - description: Predicted secreted brorin-family protein with an intact chordin-like cysteine-rich core. By family inference only, a BMP signalling antagonist, expressed in retina and brain. Untested. directly_involved_in: - id: GO:0030514 label: negative regulation of BMP signaling pathway locations: - id: GO:0005576 label: extracellular region supported_by: - *id001 - *id003 - *id004 suggested_questions: - question: Is si:dkey-283b1.7 the TGD ohnolog of vwc2 (PANTHER), a fast-evolving VWC2L-related copy, or a separate old family branch lost in tetrapods (Ensembl Compara gives it no gar or human ortholog)? Its chromosome 3 neighbourhood shows no conserved synteny with the gar vwc2 region. A phylogeny with more non-teleost fish (bichir, sturgeon, bowfin, elephant shark) and a search of the gar genome for an unannotated brorin-family gene would help decide. - question: Where exactly is si:dkey-283b1.7 expressed in retina and brain, and does its domain overlap with vwc2 or vwc2l? - question: Does the protein inhibit BMP signalling, like vwc2, despite its divergent core? suggested_experiments: - hypothesis: si:dkey-283b1.7 is a secreted BMP antagonist. description: Inject si:dkey-283b1.7 mRNA and score dorsalization and pSmad1/5/8, side by side with brorin (vwc2) mRNA; test secretion of a tagged protein in cultured cells. experiment_type: overexpression / biochemical assay - hypothesis: si:dkey-283b1.7 acts in the retina. description: In situ hybridization and a CRISPR mutant with retinal histology and ERG readouts. experiment_type: expression and loss-of-function